Bromine in the structure of Solvation of the Left-Handed Hexamer D(5BRC-G-5BRC-G-5BRC- G) in Crystals Grown At Two Temperatures (pdb 1dn4)

The binding sites of Bromine atom in the structure of Solvation of the Left-Handed Hexamer D(5BRC-G-5BRC-G-5BRC- G) in Crystals Grown At Two Temperatures (pdb code 1dn4). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 1dn4 structure was solved by B.CHEVRIER, A.C.DOCK, B.HARTMANN, M.LENG, D.MORAS, M.T.THUONG, E.WESTHOF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.6 Space group P212121 a (A) 18.010 b (A) 30.880 c (A) 44.760 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Bromine Binding Sites: Bromine binding site 1 out of 6 in 1dn4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 1dn4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cbr1, A: Dg2, B: Cbr11, A: Hoh42, A: Hoh59, B: Hoh15, conact list: Atom Atom Distance (A) Br N3 A:Cbr1 4.02 Br C2 A:Cbr1 4.57 Br C6 A:Cbr1 2.79 Br N1 A:Cbr1 4.03 Br C5 A:Cbr1 1.85 Br C4 A:Cbr1 2.76 Br BR A:Cbr1 0.00 Br N4 A:Cbr1 2.99 Br O6 A:Dg2 4.82 Br N3 B:Cbr11 4.78 Br C5 B:Cbr11 4.68 Br C4 B:Cbr11 4.08 Br BR B:Cbr11 4.44 Br N4 B:Cbr11 3.50 Br O A:Hoh42 3.95 Br O A:Hoh59 4.29 Br O B:Hoh15 4.19 interactive model: Bromine binding site 2 out of 6 in 1dn4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 1dn4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg2, A: Cbr3, A: Dg4, B: Cbr9, A: Hoh20, A: Hoh29, A: Hoh61, A: Hoh71, conact list: Atom Atom Distance (A) Br N9 A:Dg2 3.61 Br N3 A:Dg2 4.35 Br C3' A:Dg2 4.94 Br C8 A:Dg2 3.77 Br C2 A:Dg2 4.97 Br C6 A:Dg2 4.81 Br C5 A:Dg2 4.05 Br C1' A:Dg2 4.18 Br N7 A:Dg2 4.12 Br C4 A:Dg2 3.82 Br C2' A:Dg2 3.88 Br N3 A:Cbr3 3.93 Br C2 A:Cbr3 4.49 Br C6 A:Cbr3 2.69 Br N1 A:Cbr3 3.94 Br C5 A:Cbr3 1.74 Br C4 A:Cbr3 2.80 Br BR A:Cbr3 0.00 Br N4 A:Cbr3 3.16 Br O6 A:Dg4 4.26 Br N3 B:Cbr9 4.95 Br C5 B:Cbr9 4.95 Br C4 B:Cbr9 4.33 Br BR B:Cbr9 4.97 Br N4 B:Cbr9 3.73 Br O A:Hoh20 4.28 Br O A:Hoh29 3.61 Br O A:Hoh61 3.64 Br O A:Hoh71 3.95 interactive model: Bromine binding site 3 out of 6 in 1dn4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 1dn4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg4, A: Cbr5, A: Dg6, B: Cbr7, A: Hoh16, B: Hoh60, conact list: Atom Atom Distance (A) Br N9 A:Dg4 3.85 Br N3 A:Dg4 4.57 Br C8 A:Dg4 4.06 Br C6 A:Dg4 4.85 Br C5 A:Dg4 4.08 Br C1' A:Dg4 4.37 Br N7 A:Dg4 4.20 Br C4 A:Dg4 4.01 Br C2' A:Dg4 3.97 Br N3 A:Cbr5 4.03 Br C2 A:Cbr5 4.60 Br C6 A:Cbr5 2.84 Br N1 A:Cbr5 4.06 Br C5 A:Cbr5 1.81 Br C4 A:Cbr5 2.76 Br BR A:Cbr5 0.00 Br N4 A:Cbr5 3.04 Br O6 A:Dg6 4.75 Br C5 B:Cbr7 4.81 Br C4 B:Cbr7 4.28 Br BR B:Cbr7 4.71 Br N4 B:Cbr7 3.69 Br O A:Hoh16 4.05 Br O B:Hoh60 3.59 interactive model: Bromine binding site 4 out of 6 in 1dn4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 1dn4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cbr5, B: Cbr7, B: Dg8, B: Hoh57, B: Hoh60, B: Hoh66, conact list: Atom Atom Distance (A) Br N3 A:Cbr5 4.86 Br C5 A:Cbr5 4.73 Br C4 A:Cbr5 4.16 Br BR A:Cbr5 4.71 Br N4 A:Cbr5 3.62 Br N3 B:Cbr7 4.04 Br C2 B:Cbr7 4.58 Br C6 B:Cbr7 2.75 Br N1 B:Cbr7 3.99 Br C5 B:Cbr7 1.75 Br C4 B:Cbr7 2.81 Br BR B:Cbr7 0.00 Br N4 B:Cbr7 3.03 Br O6 B:Dg8 4.58 Br O B:Hoh57 4.88 Br O B:Hoh60 3.76 Br O B:Hoh66 4.42 interactive model: Bromine binding site 5 out of 6 in 1dn4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Bromine in the PDB 1dn4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cbr3, B: Dg8, B: Cbr9, B: Dg10, A: Hoh61, conact list: Atom Atom Distance (A) Br N3 A:Cbr3 4.87 Br C5 A:Cbr3 4.90 Br C4 A:Cbr3 4.24 Br BR A:Cbr3 4.97 Br N4 A:Cbr3 3.65 Br N9 B:Dg8 3.66 Br N3 B:Dg8 4.28 Br C3' B:Dg8 4.86 Br C8 B:Dg8 3.94 Br C2 B:Dg8 4.95 Br C6 B:Dg8 4.80 Br C5 B:Dg8 4.00 Br C1' B:Dg8 4.08 Br N7 B:Dg8 4.17 Br C4 B:Dg8 3.83 Br C2' B:Dg8 3.71 Br N3 B:Cbr9 4.10 Br C2 B:Cbr9 4.61 Br C6 B:Cbr9 2.80 Br N1 B:Cbr9 4.04 Br C5 B:Cbr9 1.82 Br C4 B:Cbr9 2.82 Br BR B:Cbr9 0.00 Br N4 B:Cbr9 3.09 Br C6 B:Dg10 4.94 Br O6 B:Dg10 4.08 Br O A:Hoh61 4.16 interactive model: Bromine binding site 6 out of 6 in 1dn4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Bromine in the PDB 1dn4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cbr1, B: Dg10, B: Cbr11, B: Dg12, B: Hoh15, conact list: Atom Atom Distance (A) Br N3 A:Cbr1 4.94 Br C5 A:Cbr1 4.49 Br C4 A:Cbr1 4.18 Br BR A:Cbr1 4.44 Br N4 A:Cbr1 3.67 Br N9 B:Dg10 3.64 Br N3 B:Dg10 4.57 Br C3' B:Dg10 4.98 Br C8 B:Dg10 3.98 Br C5 B:Dg10 4.31 Br C1' B:Dg10 4.12 Br N7 B:Dg10 4.29 Br C4 B:Dg10 4.01 Br C2' B:Dg10 3.73 Br N3 B:Cbr11 4.02 Br C2 B:Cbr11 4.61 Br C6 B:Cbr11 2.79 Br N1 B:Cbr11 4.10 Br C5 B:Cbr11 1.85 Br C4 B:Cbr11 2.78 Br BR B:Cbr11 0.00 Br N4 B:Cbr11 3.11 Br O6 B:Dg12 4.67 Br O B:Hoh15 4.35 interactive model: